Kinetics of charged polymer collapse: effects of additional salt

Abstract

Extensive molecular dynamics simulations, using simple charged polymer models, have been employed to probe the kinetics and dynamics of early-stage collapse of charged polymers and the effect of additional monovalent salt on such kinetics. The exponents characterizing the coarsening dynamics during such early-collapse stage via finite size scaling for the case of charged polymers are found to be different from the neutral polymers, suggesting that the collapse kinetics of charged polymers are inherently different from that neutral polymers. The kinetics of coarsening of the clusters along the collapsed trajectory also depends significantly on the counterion valency and for higher valency counterions, multiple regimes are observed and unlike the neutral polymer case, the collapse kinetics are a function of charge density along the charged polymer. Inclusion of additional salt affects the kinetics and conformational landscape along the collapse trajectory. Addition of salt increases the value of critical charge density required to initiate collapse for all the counterion valencies, though the effect is more pronounced for monovalent counterion systems. The addition of salt significantly affects the collapse trajectory in the presence of trivalent counterions via promotion of transient long-distance loop structures inducing a parallel and hierarchical local collapsed conformation leading to faster global collapsed states. This may play a role in understanding the fast folding rates of biopolymers such as proteins and RNA from extended state to a collapsed state in the presence of multivalent counterions before reorganizing into a native fold.